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I have to clone a linux drive to a smaller destination disk. By default Clonezilla will not let me do this.

This is how things look like now:
Source system:
/dev/sda1 72G 10G 58G 15% /
udev 7.9G 4.0K 7.9G 1% /dev
tmpfs 3.2G 332K 3.2G 1% /run
none 5.0M 0 5.0M 0% /run/lock
none 7.9G 0 7.9G 0% /run/shm

Destination system:
/dev/sda3 912G 49G 817G 6% /
udev 7.9G 4.0K 7.9G 1% /dev
tmpfs 3.2G 332K 3.2G 1% /run
none 5.0M 0 5.0M 0% /run/lock
none 7.9G 0 7.9G 0% /run/shm
/dev/sda2 90M 24M 61M 29% /boot
/dev/sda6 1.9G 35M 1.8G 2% /tmp

The partition has a linux unstallation on it .Source drive is 3TB, destination drive is 1TB. Therefore what I am going to do is to clone the partition sda1 from the source drive, and then restore it on the smaller disk in place of partition sda3.
What bothers me is , if I do it this way, will the restored system work normally and will it, for example start using /tmp the way it is used on the source system (eg., not using the odd 2GB tmp partition that it uses now) ? Will i need to edit /etc/fstab or the GRUB menu?

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You can first shrink your source partitions with parted/resize2fs. You can make it smaller than you need to, and then regrow on the target disk.

In your readout BTW, the source looks smaller. Or am I missing something?

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You can override the partition size check in the restore disk, advanced menu. As long as the actual partitions in the image will fit on the target drive, this will work.

For example, If you have a 250GB drive with a 100M and a 60GB partitions, you can use this to restore the image to 80GB drive. This will work because the total size of actual partitions consumes less the space on the target drive.

NOTE: Everything on the target drive will be over written and replaced with the partitions in the image.

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